7. Nextflow pipeline outputs

1 Results folder
2 Nextflow log, metrics and reports

Results folder

The results are output in the folder name specified in the .nexftlow.config file under the outdir parameter. It is generally set to be results.

params {
  outdir = 'results'
}

Nextflow log, metrics and reports

By default, Nextflow will create a log file in the working directory called .nextflow.log. This file is hidden but you can see it using the command:

ls -a

If you rerun the pipeline in the same folder, the previous .nextflow.log will be renamed .nextflow.log.1 and a new .nextflow.log will be generated.

You can change the default location by specifying a different location

nextflow -log ~/code/nextflow.log run

You can list the execution logs of previous invocations of all pipelines in a directory by running the command:

If we want to get more information about an individual run we can add the run name or session ID to the log command.

For example:

Generate an html run report

Run the following command: